Scientific

MK5 Microarray Data

Affected Genes - Ontology Breakdown - Gene Enrichment - Proteome Analysis

These are the micro-array results of a differential gene expression microarray experiments and the subsequent analysis steps performed on them. The up/down- regulation ratio was obtained by measuring WT cells against MK5 activated cells. See material and methods for technical information as well as the data usage policy.

MK5 Proteome Analysis

Table 3: Type II network, divided ranks. This table presents the output of the simulation of a type-II network in which we relied on the high confidence interactions and micro-array results. The output of the micro-array was then ranked and these ranks used as input into the network simulation. After performing two such simulations (one for the MK5 off and one for the MK5 on microarray output), we divided the ranks and sorted the results accordingly. The output of this technique is a collection of proteins that cluster naturally together.

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Rank Gene description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison

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Showing element 3530 to 3579 of 29840 in total

Interaction Map

: High confidence

Rank	description	Value Type	Network Comparison Type	Filtered	red	green	network_comparison
221	proto-oncogene tyrosine-protein kinase fyn (ec 2.7.1.112) (p59-fyn) (syn) (slk). [swissprot;acc:p06241]	Measured	Subtracted	1	6417.18	7859.6	1442.42
	putative nucleoside diphosphate kinase (ec 2.7.4.6) (ndk) (ndp kinase). [swissprot;acc:o60361]	Measured	Divided	0	1905.84	1643	1.15998
	septin 7 (cdc10 protein homolog). [swissprot;acc:q16181]	Rooted	Subtracted	1	113.374	123.463	10.089
	sirtuin 7; sir2-related protein type 7; sirtuin type 7; sirtuin (silent mating type information regulation 2, s.cerevisiae, homolog) 7; silent mating type information regulation 2, s.cerevisiae, homolog 7; sirtuin silent mating type information regulation 2 homolog 7 (s. cerevisiae). [refseq;acc:nm_016538]		Subtracted	0	42.9302	40.4104	2.5198
	spliceosomal u5 snrnp-specific 15 kda protein (dim1 protein homolog) (thioredoxin-like u5 snrnp protein u5-15kd). [swissprot;acc:o14834]		Divided	1	56.9506	64.7888	1.13763
	tata box binding protein-associated factor, rna polymerase ii, q; taf7-like rna polymerase ii, tata box binding protein (tbp)-associated factor, 50 kd; tbp-associated factor, rna polymerase ii, q. [refseq;acc:nm_024885]	Squared	Subtracted	1	57579.2	46497.2	11082
	tubby protein homolog. [swissprot;acc:p50607]	Rooted	Divided	0	39.7788	45.0452	1.13239
222	40s ribosomal protein s15 (rig protein). [swissprot;acc:p11174]	Ranked			12183	11013.2	1.10622
	40s ribosomal protein s2 (s4) (llrep3 protein). [swissprot;acc:p15880]	Measured			1499.4	1735.23	1.15728
	60s ribosomal protein l14 (cag-isl 7). [swissprot;acc:p50914]	Ranked	Subtracted	1	242.153	266.673	24.52
	chromatin assembly factor 1 subunit c (caf-1 subunit c) (chromatin assembly factor i p48 subunit) (caf-i 48 kda subunit) (caf-ip48) (retinoblastoma binding protein p48) (retinoblastoma-binding protein 4) (rbbp-4) (msi1 protein homolog). [swissprot;acc:q09028]	Rooted	Divided	1	52.7936	60.0592	1.13762
	cleavage stimulation factor, 64 kda subunit (cstf 64 kda subunit) (cf-1 64 kda subunit). [swissprot;acc:p33240]	Squared		0	410.662	561.35	1.36694
	cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418]	Measured		1	41482.5	33356.5	1.24361
	dj756n5.1.1 (continues in em:al133324 as dj1161h23.3) (fragment). [sptrembl;acc:q9h430]	Ranked		1	112	126	1.125
	hepatitis c virus core-binding protein 6; cervical cancer oncogene 3. [refseq;acc:nm_023934]	Rooted	Subtracted	0	23.5797	26.096	2.5163
	keratin associated protein 2-4; keratin associated protein 2.4. [refseq;acc:nm_033184]	Measured		0	1225.09	1079.36	145.73
	lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [refseq;acc:nm_022075]	Rooted		1	61.6639	71.7355	10.0716
	metalloprotease 1; metalloprotease 1 (pitrilysin family). [refseq;acc:nm_014889]	Squared			29570.7	18601.8	10968.9
	proto-oncogene tyrosine-protein kinase fgr (ec 2.7.1.112) (p55-fgr) (c-fgr). [swissprot;acc:p09769]	Measured			6417.18	7859.6	1442.42
	segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [swissprot;acc:o14640]	Ranked		0	5673.33	6797.56	1124.23
		Rooted	Divided	0	58.6947	51.8401	1.13223
	signal transducing adaptor molecule 2; stam-like protein containing sh3 and itam domains 2. [refseq;acc:nm_005843]	Squared	Divided	1	86281	65058.3	1.32621
	ubiquitin-conjugating enzyme e2-18 kda ubch7 (ec 6.3.2.19) (ubiquitin- protein ligase) (ubiquitin carrier protein) (ubcm4) (e2-f1) (l-ubc). [swissprot;acc:p51966]		Subtracted	0	1742.44	1500.84	241.6
223	60s ribosomal protein l22 (epstein-barr virus small rna associated protein) (eber associated protein) (eap) (heparin binding protein hbp15). [swissprot;acc:p35268]			0	374.181	141.849	232.332
	beta-1,4 mannosyltransferase. [refseq;acc:nm_019109]			1	29567	18601.6	10965.4
	brain protein 16. [refseq;acc:nm_016458]	Rooted	Divided	0	38.9679	44.0549	1.13054
	cytohesin 4. [swissprot;acc:q9uia0]	Measured	Divided	1	41482.5	33356.5	1.24361
	dc11 protein. [refseq;acc:nm_020186]	Rooted	Subtracted	0	23.5797	26.096	2.5163
	hsp90 co-chaperone cdc37 (hsp90 chaperone protein kinase-targeting subunit) (p50cdc37). [swissprot;acc:q16543]	Measured	Divided		750.981	650.724	1.15407
	keratin associated protein 1.5. [refseq;acc:nm_031957]	Measured	Subtracted		1225.09	1079.36	145.73
	maguk p55 subfamily member 2 (mpp2 protein) (discs, large homolog 2). [swissprot;acc:q14168]	Ranked	Subtracted		14257.4	13134.5	1122.9
	melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801]	Rooted	Divided	1	137.446	120.823	1.13758
	myosin heavy chain, skeletal muscle, extraocular (myhc-eo). [swissprot;acc:q9ukx3]	Ranked		1	112	126	1.125
	pnas-18. [sptrembl;acc:q9bzu3]	Ranked		0	12602.7	13939.6	1.10608
	septin 6. [swissprot;acc:q14141]	Rooted	Subtracted	1	113.169	123.23	10.061
	serine racemase (ec 5.1.1.-). [swissprot;acc:q9gzt4]	Ranked	Subtracted	1	242.153	266.673	24.52
	sh2 domain binding protein 1; tpr-containing, sh2-binding phosphoprotein. [refseq;acc:nm_014633]	Squared	Divided	0	952.068	697.024	1.3659
	t-complex protein 1, alpha subunit (tcp-1-alpha) (cct-alpha). [swissprot;acc:p17987]	Squared	Divided	1	40982.6	54272.3	1.32428
	tyrosine-protein kinase abl2 (ec 2.7.1.112) (tyrosine kinase arg). [swissprot;acc:p42684]	Measured	Subtracted	1	6417.18	7859.59	1442.41
224	5,6-dihydroxyindole-2-carboxylic acid oxidase precursor (ec 1.14.18.-) (dhica oxidase) (tyrosinase-related protein 1) (trp-1) (trp1) (trp) (catalase b) (glycoprotein-75) (melanoma antigen gp75). [swissprot;acc:p17643]	Ranked		0	14930.6	16053	1122.4
	60s ribosomal protein l23a. [swissprot;acc:p29316]	Rooted		0	22.6514	25.1571	2.5057
	60s ribosomal protein l34. [swissprot;acc:p49207]	Ranked		1	242.153	266.673	24.52
	60s ribosomal protein l7. [swissprot;acc:p18124]	Measured	Divided	0	1915.27	2206.07	1.15183
	alcohol dehydrogenase class iii chi chain (ec 1.1.1.1) (glutathione- dependent formaldehyde dehydrogenase) (ec 1.2.1.1) (fdh). [swissprot;acc:p11766]	Rooted			26.1198	23.1206	1.12972
	atp-dependent clp protease atp-binding subunit clpx-like, mitochondrial precursor. [swissprot;acc:o76031]	Ranked			9815.6	8889.93	1.10413
	cell adhesion molecule with homology to l1cam precursor; neural cell adhesion molecule; cell adhesion molecule l1-like; l1 cell adhesion molecule 2. [refseq;acc:nm_006614]	Squared			399.199	542.77	1.35965
	cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739]	Measured		1	41482.5	33356.5	1.24361
	dna polymerase epsilon p12 subunit (dna polymerase epsilon subunit 4). [swissprot;acc:q9nr33]	Rooted	Subtracted		44.849	54.7964	9.9474
	galectin-4 (lactose-binding lectin 4) (l-36 lactose binding protein) (l36lbp) (antigen ny-co-27). [swissprot;acc:p56470]	Squared	Subtracted		46021.4	56813.2	10791.8
	hepatocellular carcinoma-associated protein hca3. [refseq;acc:nm_138703]	Rooted	Divided		137.446	120.823	1.13758

Legend:
- Rank is the rank after comparing the two networks
- Gene is the ensembl human gene identifier measured by 1 or more probes on the microarray
- Value Type describes how the microarray measurement was processed. Ranked indicates that we sorted all measurements and use the rank as red and green value. Measured is the normal measurement. Squared and Rooted are the square and square root respecitcely. This might be valueable to compensate for non linear light distributions.
- Network Comparison Type describes whether we divided the red and green types or whether we sutractcted them
- Interaction Map specifies whether we used only the hig hconfidence protein-protein interactions or also included the low confidence interactions.
- Filtered specifies whether we only included the high confidence microarry measurements or not.

- http://analysis.yellowcouch.org/